1 | /* |
2 | * HDF5_loader_vector_dist.hpp |
3 | * |
4 | * Created on: May 1, 2017 |
5 | * Author: i-bird |
6 | */ |
7 | |
8 | #ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ |
9 | #define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ |
10 | |
11 | #include "Packer_Unpacker/Pack_selector.hpp" |
12 | #include "Packer_Unpacker/Packer.hpp" |
13 | #include "Packer_Unpacker/Unpacker.hpp" |
14 | |
15 | template <> |
16 | class HDF5_writer<VECTOR_DIST> |
17 | { |
18 | public: |
19 | |
20 | template<typename vector_pos_type, typename vector_prp_type> |
21 | inline void save(const std::string & filename, |
22 | const vector_pos_type & v_pos, |
23 | const vector_prp_type & v_prp) const |
24 | { |
25 | Vcluster<> & v_cl = create_vcluster(); |
26 | |
27 | //Pack_request vector |
28 | size_t req = 0; |
29 | |
30 | //std::cout << "V_pos.size() before save: " << v_pos.size() << std::endl; |
31 | |
32 | //Pack request |
33 | Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::packRequest(v_pos,req); |
34 | Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::packRequest(v_prp,req); |
35 | |
36 | // allocate the memory |
37 | HeapMemory pmem; |
38 | //pmem.allocate(req); |
39 | ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(req,pmem)); |
40 | mem.incRef(); |
41 | |
42 | //Packing |
43 | |
44 | Pack_stat sts; |
45 | |
46 | Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::pack(mem,v_pos,sts); |
47 | Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::pack(mem,v_prp,sts); |
48 | |
49 | /***************************************************************** |
50 | * Create a new file with default creation and access properties.* |
51 | * Then create a dataset and write data to it and close the file * |
52 | * and dataset. * |
53 | *****************************************************************/ |
54 | |
55 | int mpi_rank = v_cl.getProcessUnitID(); |
56 | int mpi_size = v_cl.getProcessingUnits(); |
57 | |
58 | MPI_Comm comm = v_cl.getMPIComm(); |
59 | MPI_Info info = MPI_INFO_NULL; |
60 | |
61 | // Set up file access property list with parallel I/O access |
62 | |
63 | hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS); |
64 | H5Pset_fapl_mpio(plist_id, comm, info); |
65 | |
66 | // Create a new file collectively and release property list identifier. |
67 | hid_t file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id); |
68 | H5Pclose(plist_id); |
69 | |
70 | size_t sz = pmem.size(); |
71 | //std::cout << "Pmem.size: " << pmem.size() << std::endl; |
72 | openfpm::vector<size_t> sz_others; |
73 | v_cl.allGather(sz,sz_others); |
74 | v_cl.execute(); |
75 | |
76 | size_t sum = 0; |
77 | |
78 | for (size_t i = 0; i < sz_others.size(); i++) |
79 | sum += sz_others.get(i); |
80 | |
81 | //Size for data space in file |
82 | hsize_t fdim[1] = {sum}; |
83 | |
84 | //Size for data space in file |
85 | hsize_t fdim2[1] = {(size_t)mpi_size}; |
86 | |
87 | //Create data space in file |
88 | hid_t file_dataspace_id = H5Screate_simple(1, fdim, NULL); |
89 | |
90 | //Create data space in file |
91 | hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL); |
92 | |
93 | //Size for data space in memory |
94 | hsize_t mdim[1] = {pmem.size()}; |
95 | |
96 | //Create data space in memory |
97 | hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL); |
98 | |
99 | //Create data set in file |
100 | hid_t file_dataset = H5Dcreate (file, "vector_dist" , H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); |
101 | |
102 | //Create data set 2 in file |
103 | hid_t file_dataset_2 = H5Dcreate (file, "metadata" , H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); |
104 | |
105 | //H5Pclose(plist_id); |
106 | H5Sclose(file_dataspace_id); |
107 | H5Sclose(file_dataspace_id_2); |
108 | |
109 | hsize_t block[1] = {pmem.size()}; |
110 | |
111 | //hsize_t stride[1] = {1}; |
112 | |
113 | hsize_t count[1] = {1}; |
114 | |
115 | hsize_t offset[1] = {0}; |
116 | |
117 | for (int i = 0; i < mpi_rank; i++) |
118 | { |
119 | if (mpi_rank == 0) |
120 | { |
121 | /* coverity[dead_error_line] */ |
122 | offset[0] = 0; |
123 | } |
124 | else |
125 | {offset[0] += sz_others.get(i);} |
126 | } |
127 | |
128 | int metadata[mpi_size]; |
129 | |
130 | for (int i = 0; i < mpi_size; i++) |
131 | metadata[i] = sz_others.get(i); |
132 | |
133 | //Select hyperslab in the file. |
134 | file_dataspace_id = H5Dget_space(file_dataset); |
135 | H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block); |
136 | |
137 | file_dataspace_id_2 = H5Dget_space(file_dataset_2); |
138 | |
139 | |
140 | //Create property list for collective dataset write. |
141 | plist_id = H5Pcreate(H5P_DATASET_XFER); |
142 | H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE); |
143 | |
144 | //Write a data set to a file |
145 | H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer()); |
146 | |
147 | //Write a data set 2 to a file |
148 | H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata); |
149 | |
150 | |
151 | //Close/release resources. |
152 | H5Dclose(file_dataset); |
153 | H5Sclose(file_dataspace_id); |
154 | H5Dclose(file_dataset_2); |
155 | H5Sclose(file_dataspace_id_2); |
156 | H5Sclose(mem_dataspace_id); |
157 | H5Pclose(plist_id); |
158 | H5Fclose(file); |
159 | mem.decRef(); |
160 | delete &mem; |
161 | } |
162 | |
163 | /*! \brief Return the equivalent HDF5 type for T |
164 | * |
165 | * \return The HDF5 type equivalent to T |
166 | * |
167 | */ |
168 | template<typename T> |
169 | hid_t getType() |
170 | { |
171 | if (std::is_same<T,float>::value) |
172 | {return H5T_IEEE_F32LE;} |
173 | else if (std::is_same<T,double>::value) |
174 | {return H5T_IEEE_F64LE;} |
175 | else if (std::is_same<T,char>::value || std::is_same<T,unsigned char>::value) |
176 | {return H5T_STD_I8LE;} |
177 | else if (std::is_same<T,short>::value || std::is_same<T,unsigned short>::value) |
178 | {return H5T_STD_I16LE;} |
179 | else if (std::is_same<T,int>::value || std::is_same<T,unsigned int>::value) |
180 | {return H5T_STD_I32LE;} |
181 | else if (std::is_same<T,long int>::value || std::is_same<T,unsigned long int>::value) |
182 | {return H5T_STD_I64LE;} |
183 | } |
184 | |
185 | /*! \brief It add an attribute to an already opened file |
186 | * |
187 | * \param dataset_id dataset_id |
188 | * \param name_ name of the attribute |
189 | * \param att_ attribute value |
190 | */ |
191 | template<typename value_type> |
192 | void addAttributeHDF5(hid_t dataset_id, std::string name_, value_type att_) |
193 | { |
194 | //create the data space for the scalar attibute |
195 | hid_t dataspace_id = H5Screate(H5S_SCALAR); |
196 | |
197 | //create the dataset attribute (H5T_IEEE_F64BE: 64-bit float little endian) |
198 | hid_t attribute_id = H5Acreate2(dataset_id, name_.c_str(), H5T_IEEE_F32LE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT); |
199 | //write the attibute data |
200 | herr_t status = H5Awrite(attribute_id,H5T_NATIVE_DOUBLE, &att_); |
201 | //close the attribute |
202 | status = H5Aclose(attribute_id); |
203 | //close the dataspace |
204 | status = H5Sclose(dataspace_id); |
205 | } |
206 | |
207 | /*! \brief It add an attribute to an already opened file |
208 | * |
209 | * \param dataset_id dataset_id |
210 | * \param name_ name of the attribute |
211 | * \param att_ attribute value |
212 | */ |
213 | template<typename value_type> |
214 | void addAttributeHDF5(std::string filename, std::string name_, value_type att_) |
215 | { |
216 | Vcluster<> & v_cl = create_vcluster(); |
217 | MPI_Comm comm = v_cl.getMPIComm(); |
218 | MPI_Info info = MPI_INFO_NULL; |
219 | // Set up file access property list with parallel I/O access |
220 | hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS); |
221 | |
222 | hid_t file_id = H5Fopen(filename.c_str(),H5F_ACC_RDWR, plist_id); |
223 | hid_t dataset_id = H5Dopen2(file_id,"/vector_dist" , H5P_DEFAULT); |
224 | |
225 | addAttributeHDF5(dataset_id,name_.c_str(),att_); |
226 | |
227 | //close the dataset |
228 | herr_t status = H5Dclose(dataset_id); |
229 | //close the file |
230 | status = H5Fclose(file_id); |
231 | } |
232 | |
233 | }; |
234 | |
235 | |
236 | #endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ */ |
237 | |